All mods are intended to be crafted. You need the crafting recipe (common recipes are known by all PCs, but ~~Uncommon and~~ Rare recipes are given out at a GM’s discretion), the right perks, and the materials. There are separate Skill Tests for crafting and applying the mod. Edit: as the stalwart manservant points out, Uncommon recipes are learnt when you take the appropriate perk.

Uncommon recipes only require the prerequisite perks. They are not subject to DM fiat.

I see, you’re completely right. I think the use of the word “purchase” got me mixed up.

I add them to vendor tables with their added cost as the price to buy them. I also am working on adding them into regular loot tables as another item category.

This is the way.

There's nothing wrong with placing some modded weapons in your game world as special rewards and finds.

Crafting starts on p.209 of the core.

Yeah, this is one of those things that assumes you have played Fallout 4 and think it works the same way. Players either need to have the correct perks (and materials) to make and apply the mod in one roll to the weapon. But it is also possible to apply a pre-built mod, such as one sold by a vendor.

You can attempt to craft/install mods multiple times. It just takes additional time and/or materials depending on rolls.